Index

A

ABSORPTIVE ACCURATE_3D_REACTIONS

ALL_NOTIFICATIONS ALL_WARNINGS

B

BOX_TRIANGULATION_REPORT

C

CENTER_MOLECULES_ON_GRID CHECKPOINT_INFILE CHECKPOINT_ITERATIONS CHECKPOINT_OUTFILE

CHECKPOINT_REALTIME CLAMP_CONC CUSTOM_SPACE_STEP CUSTOM_TIME_STEP

D

DEGENERATE_POLYGONS DELAY DIFFUSION_CONSTANT

DIFFUSION_CONSTANT_2D DIFFUSION_CONSTANT_REPORT

F

FILE_OUTPUT_REPORT

FINAL_SUMMARY

H

HIGH_PROBABILITY_THRESHOLD

HIGH_REACTION_PROBABILITY

I

INTERACTION_RADIUS ITERATION_REPORT

ITERATIONS

L

LIFETIME_THRESHOLD LIFETIME_TOO_SHORT

LOCATION

M

MAXIMUM_STEP_LENGTH MICROSCOPIC_REVERSIBILITY MISSED_REACTION_THRESHOLD MISSED_REACTIONS

MISSING_SURFACE_ORIENTATION MODE MOLECULE_COLLISION_REPORT

N

NEGATIVE_DIFFUSION_CONSTANT NEGATIVE_REACTION_RATE NOTIFICATIONS

NUMBER_OF_TRAINS, [1] NUMBER_TO_RELEASE

P

PARTITION_LOCATION_REPORT PARTITION_X PARTITION_Y PARTITION_Z

PROBABILITY_REPORT PROBABILITY_REPORT_THRESHOLD PROGRESS_REPORT

R

RADIAL_DIRECTIONS RADIAL_SUBDIVISIONS REFLECTIVE RELEASE_EVENT_REPORT

RELEASE_INTERVAL RELEASE_PATTERN RELEASE_PROBABILITY ROTATE

S

SCALE SHAPE

SPACE_STEP SURFACE_GRID_DENSITY

T

TARGET_ONLY TIME_STEP TIME_STEP_MAX TRAIN_DURATION

TRAIN_INTERVAL TRANSLATE TRANSPARENT

U

USELESS_VOLUME_ORIENTATION

V

VACANCY_SEARCH_DISTANCE

VARYING_PROBABILITY_REPORT

W

WARNINGS